FTL - ohcrapshieldsaredown!

[Xanthir]

That's what fire is for.

(I've never even reached the flagship on hard, let alone beat it.)

[SuicideJunkie]

Also fun is to beam rockmen into a flaming room so it can't be recaptured by the crew. If that room is the medbay, then you can lock down all the living crew into the 'safe' areas of the ship while you smash the dangerous rooms.

Breach weapons are particularly good for anti-AI work too.
The ship AIs can't repair systems with a hull breach, and before the takeover, crew have to fix the breach before they can bring the system back online, buying you extra time.

Edit:
As a bonus, if the AI is repairing a system, a fire will reset its progress. So fire beams are worth shooting even when there is no air on the target and it self-extinguishes.